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| Dataset Title: | [Montery Bay Time Series Data] - Samples collected from the Monterey Bay Times Series from May 2014 to February 2016. These data include CTD, nutrient, chlorophyll a and phaeopigment concentration data. (Differential contributions of archaeal ammonia oxidizer ecotypes in relation to their changing environment) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_774848) |
| Information: | Summary
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Attributes {
s {
Cruise {
Int32 _FillValue 2147483647;
Int32 actual_range 3416, 34915;
String bcodmo_name "unknown";
String description "Cruise identifier";
String long_name "Cruise";
String units "unitless";
}
Date {
String bcodmo_name "date_local";
String description "Date (Pacific Standard Time, PST) of sampling: YYYY-MM-DD";
String long_name "Date";
String source_name "Date";
String time_precision "1970-01-01";
String units "unitless";
}
Station {
String bcodmo_name "station";
String description "Station name (M1 or M2)";
String long_name "Station";
String units "unitless";
}
Month_Day {
String bcodmo_name "unknown";
String description "Month and day of sampling - MMM_DD";
String long_name "Month Day";
String units "unitless";
}
Year {
Int16 _FillValue 32767;
Int16 actual_range 2014, 2016;
String bcodmo_name "year";
String description "Year of sampling - YYYY";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 36.6893, 36.7663;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude - south is negative";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -122.3988, -122.0058;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude - west is negative";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 0.0, 500.0;
String axis "Z";
String bcodmo_name "unknown";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Water depth sampled (BCTD)";
String ioos_category "Location";
String long_name "Depth";
String positive "down";
String standard_name "depth";
String units "m";
}
Temperature {
Float32 _FillValue NaN;
Float32 actual_range 5.84, 18.34;
String bcodmo_name "temperature";
String description "Water temperature (BCTD)";
String long_name "Temperature";
String units "degrees Celcius (°C)";
}
Salinity {
Float32 _FillValue NaN;
Float32 actual_range 32.96, 34.24;
String bcodmo_name "sal";
Float64 colorBarMaximum 37.0;
Float64 colorBarMinimum 32.0;
String description "Water salinity (BCTD)";
String long_name "Sea Water Practical Salinity";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "psu";
}
Density {
Float32 _FillValue NaN;
Float32 actual_range 23.87, 26.96;
String bcodmo_name "density";
String description "Water density (T) - calculated";
String long_name "Density";
String units "unitless";
}
Pressure {
Float32 _FillValue NaN;
Float32 actual_range 1.01, 507.5;
String bcodmo_name "pressure";
String description "Water pressure (BCTD)";
String long_name "Pressure";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PRESPR01/";
String units "decibar (dbar)";
}
Light_Penetration_Depth {
String bcodmo_name "unknown";
String description "LPD estimated";
String long_name "Light Penetration Depth";
String units "percentage (%)";
}
Nit_rate_insitu {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 355.188;
String bcodmo_name "N";
String description "Nitrification Rate - in situ light incubation";
String long_name "Nit Rate Insitu";
String units "nanomoles per day (nM/d)";
}
Nit_rate_dark {
Float32 _FillValue NaN;
Float32 actual_range 0.012, 355.188;
String bcodmo_name "N";
String description "Nitrification Rate - dark incubation";
String long_name "Nit Rate Dark";
String units "nanomoles per day (nM/d)";
}
Chlorophyll {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 16.28;
String bcodmo_name "unknown";
Float64 colorBarMaximum 30.0;
Float64 colorBarMinimum 0.03;
String colorBarScale "Log";
String description "chlorophyll concentration";
String long_name "Concentration Of Chlorophyll In Sea Water";
String units "milligram per cubic meter (mg/m3)";
}
Phaeopigments {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 4.58;
String bcodmo_name "phaeopigment";
String description "phaeopigment concentration";
String long_name "Phaeopigments";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHAEFMP1/";
String units "milligram per cubic meter (mg/m3)";
}
Chlorophyll_a {
Float32 _FillValue NaN;
Float32 actual_range -0.02, 16.2;
String bcodmo_name "chlorophyll a";
Float64 colorBarMaximum 30.0;
Float64 colorBarMinimum 0.03;
String colorBarScale "Log";
String description "depth-integrated chlorophyll";
String long_name "Concentration Of Chlorophyll In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLHPP1/";
String units "milligram per square meter (mg/m2)";
}
Fluorescence {
Float32 _FillValue NaN;
Float32 actual_range 0.04, 3.09;
String bcodmo_name "fluorescence";
String description "chlorophyll fluorescence (BCTD)";
String long_name "Fluorescence";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/";
String units "volts";
}
PO4 {
Float32 _FillValue NaN;
Float32 actual_range 0.18, 3.31;
String bcodmo_name "PO4";
String description "phosphate concentration";
String long_name "Mass Concentration Of Phosphate In Sea Water";
String units "micromole (uM)";
}
SiO4 {
Float32 _FillValue NaN;
Float32 actual_range -0.01, 89.87;
String bcodmo_name "SiO4";
String description "silicate concentration";
String long_name "Si O4";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/SLCAAAZX/";
String units "micromole (uM)";
}
NO3 {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 40.93;
String bcodmo_name "NO3";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "nitrate concentration";
String long_name "Mole Concentration Of Nitrate In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/";
String units "micromole (uM)";
}
NO2 {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.25;
String bcodmo_name "NO2";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "nitrite concentration";
String long_name "Mole Concentration Of Nitrite In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRIAAZX/";
String units "micromole (uM)";
}
NH4 {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.37;
String bcodmo_name "Ammonium";
Float64 colorBarMaximum 5.0;
Float64 colorBarMinimum 0.0;
String description "ammonia concentration";
String long_name "Mole Concentration Of Ammonium In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
String units "micromole (uM)";
}
Total_CO2 {
Float32 _FillValue NaN;
Float32 actual_range 1959.07, 2303.24;
String bcodmo_name "TCO2";
String description "total carbon dioxide";
String long_name "Total CO2";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TCO2KG01/";
String units "millimoles per liter (mmol/L)";
}
Oxygen {
Float32 _FillValue NaN;
Float32 actual_range 0.37, 7.02;
String bcodmo_name "dissolved Oxygen";
String description "dissolved oxygen";
String long_name "Oxygen";
String units "millimoles per liter (mmol/L)";
}
Transmissivity {
Float32 _FillValue NaN;
Float32 actual_range 68.9, 92.1;
String bcodmo_name "transmission";
String description "optical clarity (BCTD)";
String long_name "Transmissivity";
String units "percentage (%)";
}
amoA_qPCR {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 5.81e+8;
String bcodmo_name "abundance";
String description "archaeal amoA gene abundance";
String long_name "Amo A Q PCR";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "copies per liter (copies/L)";
}
WCA_qPCR {
Float64 _FillValue NaN;
Float64 actual_range 941.0, 2.44e+8;
String bcodmo_name "abundance";
String description "Water column A amoA gene abundance";
String long_name "WCA Q PCR";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "copies per liter (copies/L)";
}
WCB_qPCR {
String bcodmo_name "abundance";
String description "Water column B amoA gene abundance (bdl=below detection limit)";
String long_name "WCB Q PCR";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "copies per liter (copies/L)";
}
nirKa_qPCR {
Float64 _FillValue NaN;
Float64 actual_range 4480.0, 1.12e+8;
String bcodmo_name "abundance";
String description "archaeal nirK group A gene abundance";
String long_name "Nir Ka Q PCR";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "copies per liter (copies/L)";
}
nirKb_qPCR {
Float64 _FillValue NaN;
Float64 actual_range 12400.0, 1.68e+8;
String bcodmo_name "abundance";
String description "archaeal nirK group B gene abundance";
String long_name "Nir Kb Q PCR";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "copies per liter (copies/L)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"The water column in Monterey Bay (coastal California, USA) was sampled near-
monthly from May 2014-February 2016 at stations M1 (36.747 \\u00baN, 122.022
\\u00baW) and M2 (36.697 \\u00baN, 122.378 \\u00baW), on board the RV Western
Flyer or RV Rachel Carson using a CTD Rosette sampler (Sea-Bird Scientific,
Bellevue, WA). For each hydrocast, the CTD collected data on conductivity,
temperature, depth, dissolved oxygen (DO), total CO2, and transmissivity
(turbidity). Additional samples were collected from 11-12 depths from the cast
(0, 5, 10, 20, 30, 40, 60, 80, 100, 150, 200 m; 500 m included for 2015-2016)
to measure nutrients (ammonia, nitrite, nitrate, silicate, phosphate),
chlorophyll a and phaeopigment concentrations. These were processed using
established methods as part of the Monterey Bay Time Series
([http://www3.mbari.org/bog/Projects/CentralCal/summary/ts_methods_and_materials.htm](\\\\\"http://www3.mbari.org/bog/Projects/CentralCal/summary/ts_methods_and_materials.htm\\\\\");
Pennington and Chavez 2000). Light penetration depth (LPD; 0.1-50 % of surface
light) was estimated by secchi disk.
Approximately 1 L sample seawater was filtered using a peristaltic pump onto
duplicate filters \\u2013 10 \\u00b5m polycarbonate (PCTE, Sterlitech; pre-
filter), 0.2 \\u00b5m GVWP (Millipore; final filter) \\u2013 for molecular
analysis from 6-10 depths per site per month (0-500 m depth). Samples were
immediately frozen on liquid N2 and stored at -80\\u00b0C upon return to
laboratory until processing.
DNA was co-extracted with RNA using previously described methods (Smith et al.
2014a), with slight modification \\u2013 both 0.1 and 0.5 mm sterile glass
beads (BioSpec) were used for bead beating on the FastPrep (Thermo) and fresh
-mercaptoethanol was added to Lysis/Binding buffer (10 \\u00b5L per mL)
immediately before extraction. Concentration of DNA was measured using a Qubit
fluorometer (Invitrogen). Gene abundance was determined using published
methods for total archaeal amoA (Francis et al. 2005), water column group A
(WCA) and water column group B (WCB) amoA (Beman et al. 2008); modified to
TaqMan assay, (Mosier and Francis 2011), and two archaeal nirK groups (AnirKa
and AnirKb; Lund et al. 2012).\\u00a0
Water samples were collected from 6-10 depths for nitrification rate
measurements using 15NH4Cl as a tracer. Sample seawater was spiked with
15NH4Cl, and placed in ship-board seawater flow-through incubators for 24 h.
Incubations were carried out in the dark or at estimated in situ light using
stainless steel tubes with pre-drilled evenly spaced and sized holes
(Pennington and Chavez 2000; Smith et al. 2014). At the end of incubations,
samples were filtered (0.2 \\u00b5m) and frozen at -20 \\u00baC. \\u03b415N
values were measured from NOx in each sample, converted to N2O via the
bacterial denitrification assay (Sigman et al. 2001) using a ThermoFinnigan
Gas Bench and PreCon trace gas concentration system interfaced with the Delta
VPLUS isotope-ratio mass spectrometer (Bremen, Germany) at the UC Davis Stable
Isotope Facility.";
String awards_0_award_nid "555576";
String awards_0_award_number "OCE-1357024";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1357024";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "Michael E. Sieracki";
String awards_0_program_manager_nid "50446";
String cdm_data_type "Other";
String comment
"Cruise data
PI: Christopher Francis
Data Version 1: 2019-08-13";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2019-08-07T18:20:38Z";
String date_modified "2020-02-03T21:02:45Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.774848.1";
Float64 Easternmost_Easting -122.0058;
Float64 geospatial_lat_max 36.7663;
Float64 geospatial_lat_min 36.6893;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -122.0058;
Float64 geospatial_lon_min -122.3988;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 500.0;
Float64 geospatial_vertical_min 0.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-21T11:26:22Z (local files)
2024-11-21T11:26:22Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_774848.html";
String infoUrl "https://www.bco-dmo.org/dataset/774848";
String institution "BCO-DMO";
String instruments_0_acronym "CTD Sea-Bird";
String instruments_0_dataset_instrument_nid "775390";
String instruments_0_description "Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/130/";
String instruments_0_instrument_name "CTD Sea-Bird";
String instruments_0_instrument_nid "447";
String instruments_0_supplied_name "CTD Rosette sampler (Sea-Bird Scientific, Bellevue, WA)";
String keywords "ammonia, ammonium, amo, amoA_qPCR, bco, bco-dmo, biological, carbon, carbon dioxide, chemical, chemistry, chlorophyll, Chlorophyll_a, co2, concentration, concentration_of_chlorophyll_in_sea_water, cruise, dark, data, dataset, date, day, density, depth, dioxide, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Salinity/Density > Salinity, erddap, fluorescence, insitu, latitude, light, Light_Penetration_Depth, longitude, management, mass, mass_concentration_of_phosphate_in_sea_water, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, month, Month_Day, n02, nh4, nir, nirKa_qPCR, nirKb_qPCR, nit, Nit_rate_dark, Nit_rate_insitu, nitrate, nitrite, NO2, no3, O2, ocean, oceanography, oceans, office, oxygen, pcr, penetration, phaeopigments, phosphate, po4, practical, preliminary, pressure, rate, salinity, science, sea, sea_water_practical_salinity, seawater, SiO4, station, temperature, time, total, Total_CO2, transmissivity, water, wca, WCA_qPCR, wcb, WCB_qPCR, year";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/774848/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/774848";
Float64 Northernmost_Northing 36.7663;
String param_mapping "{'774848': {'Latitude': 'flag - latitude', 'Depth': 'flag - depth', 'Longitude': 'flag - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/774848/parameters";
String people_0_affiliation "Stanford University";
String people_0_person_name "Dr Christopher Francis";
String people_0_person_nid "51553";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Monterey Bay Aquarium Research Institute";
String people_1_affiliation_acronym "MBARI";
String people_1_person_name "Dr Francisco Chavez";
String people_1_person_nid "50604";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Karen Soenen";
String people_2_person_nid "748773";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Contributions of AOA Ecotypes";
String projects_0_acronym "Contributions of AOA Ecotypes";
String projects_0_description
"Description from NSF award abstract:
Because the first and rate-limiting step of nitrification, ammonia oxidation, was long believed to be restricted to a few groups within the domain Bacteria, the discovery of ammonia-oxidizing archaea (AOA) - members of one of the most abundant microbial groups on the planet (now known as the Thaumarchaeota) - has seriously challenged our understanding of the microbial ecology and biogeochemistry of the nitrogen cycle. AOA are now believed to be responsible for the majority of nitrification in the sea, and occur in the marine water column as two taxonomically distinct groups, namely the Water Column Group A (WCA) and B (WCB) ecotypes. An open question in marine biogeochemistry is whether the taxonomic definition of WCA and WCB and their observed distributions correspond to distinct ecological and biogeochemical niches. To fill this critical knowledge gap, this project will examine linkages between patterns of ecotype-specific archaeal ammonia monooxygenase (amoA) gene abundance and expression and 15N-based nitrification rates across multiple depths (0-500m) and two stations within the Monterey Bay Time Series (MBTS). Acquiring quantitative expressional and biogeochemical activity data from a wide array of water column samples from the MBTS, bimonthly over the course of two years, will yield valuable new insights into how archaeal ammonia oxidation and AOA ecotype dynamics are influenced by changes in ocean conditions.
The discovery of AOA has served to refocus attention on nitrification in the ocean; however, there are still an alarmingly low number of direct measurements of oceanic ammonia oxidation rates. This paucity of data has made it difficult to accurately quantify the degree to which nitrification supports primary production in the global ocean. One major goal of this project is to ascertain whether a quantitative relationship between the abundance of AOA genes and transcripts and instantaneous rates of nitrification exists for the coastal ocean. Prior collaboration indicated a strong correlation between 15N-based nitrification rates and archaeal amoA gene copies in surface waters of northern Monterey Bay. This study will acquire a more holistic understanding of this relationship by performing these measurements as part of the MBTS, not only at depths in the euphotic zone - where the biogeochemical importance of nitrification is hotly debated - but also within disphotic and aphotic waters of the mesopelagic. By conducting this research as part of the 23 year MBTS, the resultant dataset will be incorporated into a larger oceanographic framework. These efforts will also directly connect to a goal of the MBTS to determine spatiotemporal patterns in new and regenerated primary production by providing new quantitative insights into processes responsible for regenerated nitrogen production in the photic zone. Additionally, the extensive collections of microbial sequence and biogeochemical data generated through this study will provide a valuable resource to the scientific community and, ultimately, help reveal new information about the ecology and factors regulating nitrification in the ocean, greatly advancing our ability to model its role in N and C cycles under present and future conditions.";
String projects_0_end_date "2017-03";
String projects_0_geolocation "Monterey Bay";
String projects_0_name "Differential contributions of archaeal ammonia oxidizer ecotypes in relation to their changing environment";
String projects_0_project_nid "555577";
String projects_0_start_date "2014-04";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 36.6893;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Samples collected from the Monterey Bay Times Series from May 2014 to February 2016. These data include CTD, nutrient, chlorophyll a and phaeopigment concentration data.";
String title "[Montery Bay Time Series Data] - Samples collected from the Monterey Bay Times Series from May 2014 to February 2016. These data include CTD, nutrient, chlorophyll a and phaeopigment concentration data. (Differential contributions of archaeal ammonia oxidizer ecotypes in relation to their changing environment)";
String version "1";
Float64 Westernmost_Easting -122.3988;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.